arkansas center for plant-powered production epscor asset ii annual meeting, 2012 intro to the p3...
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ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
• Intro to the P3 Center concept• Management and logistics in Year 2• Strategic Goals – Highlights of Year 2
accomplishments
The Arkansas Center for Plant-Powered Production
(The P3 Center)
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
What is the P3 Center?
• NSF EPSCoR-supported research consortium targeting cross-disciplinary approaches to plant biology and plant products
• 5 Universities– Arkansas State University– University of AR, Fayetteville– University of AR, Little Rock– University of AR, Pine Bluff– University Central Arkansas
• > 45 faculty (plant biologists, chemists, molecular biologists, environmental scientists, plant pathologists, entomologists, food scientists, computer scientists, biochemical engineers)
NCTR
UCA
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
P3 Center Mission
To take advantage of the unique biosynthetic capacity of plants as scalable biofactories for proteins, chemicals, and biomaterials to address global challenges in energy, human health, climate change, and food security.
Our research is focused on understanding the underlying mechanisms that drive the amazing biosynthetic capacity of plants
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
Some Year 2 Logistics
• Management team – Comprised of campus leads, cluster leads, outreach coordinator– And our program managers, Emily Devereux and Lacy Nelson– Meet every 2 weeks by phone– Campus visits - faculty and administrators – P3 Lead change at UCA
(now Ben Cash, David Dussourd)
• Our Technical Advisory Committee– Rotation structure established– New chair : Kent Chapman (and many thanks to Joe Chappell!)– New members: Industry - John Howard (Adv. Biotech. Institute,
CA) and Bioinformatics - Robin Buell (Michigan State University)– Gary Thompson and Celia MacIntosh “retired” – Many thanks!!!
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
I. Build instrumentation infrastructure and capabilities
II. Enhance research competitiveness of P3 focal areas
III. Build intellectual infrastructure thru professional and workforce development
IV. Build national reputation
V. Build sustainability of the program
P3 Center Strategic Plan
Some highlights……
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
I. Instrumentation• Web database “live” by end of year • Campuses tasked with sustainability plan for multi-
user items• Highlight – the Scanalyzer - truly enabling technology
for high-thru-put phenotyping (Argelia Lorence)
– Collecting exceptional data!– Training session at ACMAP mtg– Initiated collaboration with Nebraska
EPSCoR (joint proposal to NSF pending)
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
II. Research Competitiveness Research clusters
1. Comparative metabolomics:– Steve Grace (UALR); Julie Carrier (UAF)
3. Productivity “set-points”– Beth Hood (ASU)
2. Plant interactions with other organisms
– Ken Korth (UAF)
4. Next-Gen Seq and bioinformatics– Xiuzhen Huang (ASU)
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
Metabolic Profiling
Expression Profiling
Presented at Phytochemical Society of North America and P3/ACMAP
See poster by Marissa de La Paz
Student InvolvementRyne RamakerDestiny Davis (INBRE)Delice Kayeshgiue (INBRE)Chen ChenMarissa de La Paz
Comparative metabolomics:• Gene, pathway enzyme, discovery• Metabolite engineering• HTP metabolite data management
Genetic Phenotyping
Gene Discovery
Revealed Novel Aspects of Light
Regulation of Plant Metabolism
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
Presented at MCBIOS 2012 and P3/ACMAP 2012 See poster by Stephen Embry
What is it good for? Produces rapid unbiased “barcode” of LCMS
data for statistical analysis Class assignment, detection of outliers, etc. Data mining for important variables,
biomarkers, etc.
What is it? A versatile software tool designed to parse,
filter, and mine LCMS datasets
MySql Tables runs, scan_number, and point_number
NeedleFinder Object BucketFiller()
MySql Tables bin and bucket_analysis
Export LCMS data in CDF format
MVA MetaboAnalystStatistica
Output files in csv format
NeedleFinderObject Loader()
NeedleFinder Object Parser()
Class Assignment
3D Barcode
NeedleFinder: a New Bioinformatics Tool for Mining Metabolomic Datasets
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
Plant interactions – plant proteins and metabolites serve as signals in host pathways, in
defense against pests, and to promote health and nutrition in animals
Applying tools of genomics, plant culture, and metabolomics to fungal pathogenesis, insect herbivory, food science, neurobiology, mammalian cell culture, and immunology
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
Biological “set-points” -- addressing mechanisms that limit protein and biomass accumulation
INPUTS• Genes• Genotypes• Nutrients• Conditions
OUTPUTS• Proteins• Phytochemicals• Biomass• Biomaterials
Nature has selected for metabolic efficiency
Plants make what they need – but have tremendous untapped capacity
Key Activities and Accomplishments• Held campus brainstorming meetings • Visited NSF ‘plant genome’; USDA ‘plant biology’ (plan collab. grant)• Initiated interactions with iPlant Collaborative• Submitting BMC Plant Biology/ Biotechnology “special issue” (review and 4
research articles)
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
Determined factors affecting high-level protein accumulation in transgenic maize seed—P3 seed grant Xiuzhen Huang, Thomas Teoh, Elizabeth Hood• Moved from Microarray to Next Gen Sequencing to compare high and
low protein accumulation in embryos; First Next Gen project at ASU• One manuscript submitted, one in preparation• Network proposal submitted to NSF 2010• Set Points proposal planned for USDA 2012
Stage Total # of genes expressed
S15 17,107
S21 18,177
S27 16,122
Avg. 17,105
Research Highlight
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
Next-Gen and BioInformatics• ~17 P3 projects (Just received last data sets)
• Secure data storage on P3 servers (ASU)
• Xiuzhen Huang’s students are performing initial alignment, assembly, and expression counts
• NSF-EPSCoR BioInformatics Conference (Huang & McClure)
• iPlant Workshop– May 17-18 at UALR– ~45 participants; > 20 P3– State Breakdown : AR:
34, MS: 7 (EPSCoR link), LA: 1, KY:1
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
Faculty successes and reputation building
• Invited book editors– Argelia Lorence, Recombinant Gene Expression,
Reviews and Protocols, 3rd Edition
– Burt Bluhm, Fungal Genomics: Methods and Protocols (co-ed)
– Julie Carrier, Biorefinery Co-Products: Phytochemicals, Primary Metabolites and Value-Added Biomass Processing (co-ed)
• Increased participation on grant review panels– DOE, NSF, USDA
III. Professional and Workforce Development
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
Faculty successes and reputation building
• Leadership in national organizations– e.g., Fabricio Medina-Bolivar, VP for ACMAP– EPSCoR reviewer (6 P3 members on Missouri Review)
• Entrepreneurship recognition– Cramer, Radin (BioStrategies-LC) win 2012 Tibbetts Award for
innovation from SBA (awarded in White House)
III. Professional and Workforce Development
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
P3 Student updates
• 85 UG, Grad Student, PD • Current student support
– Graduate student: 10 in Yr2; 13 in Yr3– Undergrads : 16 in Yr2; 16 in Yr3– 7 successful SURF awards (1 UCA; 2 UAF; 4 ASU)– 4 LSAMP students (1 UCA; 3 ASU)
• Accomplishments– John Ridenour (UAF) was awarded NSF Graduate Student
Research Fellowship– Walter Acosta (ASU) took 1st prize in his poster category,
National EPSCoR conference
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
Educational outreach & diversityBioTech-iN-a-Box Program• Comprehensive teaching module ($6000 equipment)• Two-week loan period; Lesson plans provided• 50+ AR Teachers certified for use
BTNB: BIOFUELSBTNB: ELECTROPHORESIS
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
Expanding Throughout AR – UAPB • Spring 2012 UG Biofuels Class:
– 10 UAPB UG Students trained as “teacher mentors” for BioTech-iN-a-Box: Biofuels (BTNB).
• Professional Development Workshop, May 31st- June 1st – 8 regional (South AR) science teachers trained/certified– Participation by UG teacher mentors
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
IV. National Reputation
P3 website is live!www.plantpoweredproduction.org
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
P3 Annual Research Symposium – joint with ACMAP
– Great science: 250 scientists, 19 countries, 22 states – P3 Participation: 28 Faculty; 61 Students/Postdocs;
12 Oral Presentations; 41 Poster Presentations. – Awards: Best Oral: Debbie Vicuna; Best Graduate
Poster: Tianhong Yang; Best Undergraduate Poster: Zach Marsh
• National Agricultural Biotechnology Council (NABC) Meeting hosted in Fayetteville, May 2012; co-organized by Ken Korth
2013 P3 Research Symposium will be held in conjunction with the Southern Section –
American Society of Plant BiologyLittle Rock, April 6-9, 2013
Mariya Khodakovskaya (UALR), host
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
V. Sustainability• More than $3 M in new grants funded• Examples of major federal award
– Qingfang He (UALR) - NSF ($451,460), Functional analysis of the high-light-inducible proteins (HLIP) in Synechocystis PCC 6803.
– Esten Mason (UAF) – USDA AFRI ($331,310), Development of physiological & genetic markers for waterlogging tolerance in wheat
– Lirong Zeng (UALR) – USDA-NIFA ($149,979) Genome-wide identification & characterization of tomato E2 ubiqutin-conjugating enzymes in plants
– Correll, Burt Bluhm (UAF), et al. – USDA-NIFA-SCRI ($827,745), Managing Downy Mildew of spinach, a genomics-based approach to the host and the pathogen
– Ioannis Tzanetakis (UAF) – United Soybean Board ($115,000), Epidemiology and identification of resistance to Soybean Vein Necrosis virus
– Carole Cramer (ASU) – NIH-R21 ($374,000), RTB-mediated delivery: Orchestrating antigen trafficking to enhance cell immunity
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
Entrepreneurship and Industry Awards• Industry Awards
– Fabricio Medina-Bolivar (ASU) – Infiniti Pharmaceuticals ($215,695), Root cultures of Veratrum californicum as a sustainable source of cyclopamine and related steroidal alkaloids
• SBIRs to P3-associated start-ups– Hood & Hood (ASU) USDA SBIR phase II to Infinite Enzymes
($450,000), Formulating new cellulases for diverse markets: Defining QA parameters
– Radin, Cramer (ASU), Medrano (ASU), USDA SBIR phase II ($460,000) to BioStrategies LC, Plant-based production of porcine IL-12
ARKANSAS CENTER FOR PLANT-POWERED PRODUCTIONEPSCoR ASSET II Annual Meeting, 2012
P3 - Continuing to build
Iterative strategic planning to ensure that the more dispersed investment in a “research network” • Builds transformational infrastructure• Empowers research in Arkansas• Brings value to its members
Thank you! Questions?